def aq_correction(entries):
"""
Applies the Materials Project Aqueous Compatibility scheme for mixing GGA
and GGA+U to a list of entries.
Removes entries which aren't compatible with the mixing scheme
Args:
entries: List of entries on which the correction will be applied
"""
#| - aq_correction
from pymatgen.entries.compatibility import MaterialsProjectAqueousCompatibility
def contains_entry(entry_list, ent):
"""
Helpful to filter duplicate entries, if entry
is in entry_list, return True
Args:
entry_list: list of pymatgen entries to consider
entry: entry which will be analyzed
"""
ent_id = ent.entry_id
ent_E = ent.energy_per_atom
ent_redfor = ent.composition.reduced_formula
for e in entry_list:
if e.entry_id == ent_id or (abs(ent_E - e.energy_per_atom) < 1e-6
and ent_redfor == e.composition.reduced_formula):
return True
aqcompat = MaterialsProjectAqueousCompatibility() #Implements the GGA/GGA+U mixing scheme,
entries_aqcorr = list()
for entry in entries:
aq_corrected_entry = aqcompat.process_entry(entry) #Corrections, if none applicable, gets rid of entry
if not contains_entry(entries_aqcorr, aq_corrected_entry): #If entry already in entries_aqcorr don't add
entries_aqcorr.append(aq_corrected_entry)
return entries_aqcorr
#__|
#NOTE This line assumes that the every entry in the experimental ion energy
# has the same ref. st. solid
ref_state = str(ion_dict[0]['Reference Solid'])
ref_dict = {ref_state: ion_dict[0]['Reference solid energy']}
# Run aqueouscorrection on the entries
# Entries without applicable corrections will be discarded
# Implements the GGA/GGA+U mixing scheme
aqcompat = MaterialsProjectAqueousCompatibility()
entries_aqcorr = list()
for entry in entries:
# Applies corrections to entry, if none applicable it gets rid of entry
aq_corrected_entry = aqcompat.process_entry(entry)
# If entry already in entries_aqcorr then don't add to list
if not contains_entry(entries_aqcorr, aq_corrected_entry):
entries_aqcorr.append(aq_corrected_entry)
# Generate a phase diagram to consider only solid entries stable in water.
pd = PhaseDiagram(entries_aqcorr)
stable_solids = pd.stable_entries
stable_solids_minus_h2o = [
entry for entry in stable_solids
if entry.composition.reduced_formula not in ["H2", "O2", "H2O", "H2O2"]
]
# +
pbx_solid_entries = []
for entry in stable_solids_minus_h2o: